Hours after the San Francisco Municipal Transportation Agency reported its delays across Muni trains citywide were cleared, inbound train service began seeing major delays — again.

Those delays were so severe Tuesday evening that BART was honoring Muni transfers so stranded riders could get to some parts of town that are covered by both Muni and BART, according to the SFMTA.

UPDATE: 3:30 P.M.:

Thousands of San Francisco commuters experienced delays across Muni on Tuesday, and operators were forced to run their trains manually due to a mechanical failure.

The source of the problem was found at Montgomery Station, and by 2:30 p.m. Muni service began to slowly restore.

“We’ve had crews there pretty much all day,” said Erica Kato, an SFMTA spokesperson.

That automatic train control system was on the fritz due to a mechanical issue, Kato said, and operators had to pilot manually through the subways — more slowly than the computers are able to go — which contributed to the delay.

Those intermittent systemwide delays were felt more deeply by some trains than others, she said. While some didn’t experience delays at all, others complained they were stuck in tunnels for quite awhile.

“I see more and more people just waiting around at west portal it’s ridiculous … you don’t give a damn about anything,” Muni rider Manuel Gonzalez wrote on Twitter to the SFMTA. “Who do I speak about a refund, I lost two hours of my shift today on top of getting a written. Not okay.”

By noon, according to SFMTA’s Twitter feed, bus shuttles were on their way to West Portal station to pick up stranded passengers.

Traditionally, Muni trains are run manually by operators when they run on the surface. The N-Judah, for instance, is piloted by a Muni operator as it traverses the Inner Sunset. When trains enter Muni tunnels and the subway system, however, they run on an automatic train control system — essentially by computer.